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Effects of Cd(Ⅱ) and Cu(Ⅱ) on microbial characteristics in 2-chlorophenol-degradation anaerobic bioreactors

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Journal of Environmental Sciences 2008年第6期20卷 745-752页

作者： HUANG Aiqun CHEN Hao CHEN Ling DAI Yalei ZHAO Jianfu State Key Laboratory of Pollution Control and Resource Reuse College of Environmental Science and Engineering Tongji University Shanghai 200092 China Department of Immunology School of Basic Medical Science Tongji University Shanghai 200092 China

The effects of Cd^2＋ and Cu^2＋ at 300 mg/L on anaerobic microbial communities that degrade 2-cholorophenol （2-CP） were examined. Based on the polymerase chain reaction （PCR） of 16S rDNA, bacterial community diversity and archaeal community structure were analyzed with denaturing gradient gel electrophoresis （DGGE） and cloning, respectively. Degradation capabilities of the anaerobic microbial community were drastically abated and the degradation efficiency of 2-CP was reduced to 60% after shock by Cu^2＋ and Cd^2＋, respectively. The bacterial community structure was disturbed and the biodiversity was reduced after shock by Cu^2＋ and Cd^2＋ for 3 d. Some new metal-resistant microbes which could cope with the new condition appeared. The sequence analysis showed that there existed common archaea species in control sludge and systems when treated with Cu^2＋ and Cd^2＋, such as Methanothrix soehngenii, Methanosaeta concilii, uncultured euryarchaeote, and so on. Both the abundance and diversity of archaeal species were altered with addition of Cd^2＋ and Cu^2＋ at high concentration. Although the abundance of the predominant archaeal species decreased with Cd^2＋ and Cu^2＋ addition for 3 d, they recovered to some extent after 10 d. The diversity of archaeal species was remarkably reduced after recovery for 10 d and the shift in archaeal composition seemed to be irreversible. The 2-CP-degradation anaerobic system was more sensitive to Cu^2＋ than Cd^2＋.

关键词： 2-cholorophenol （2-CP） Cd^2＋ Cu^2＋ microbial community diversity Bacteria archaea DGGE cloning

The structure of microbial populations in Nelore GIT reveals inter-dependency of methanogens in feces and rumen

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Journal of Animal Science and Biotechnology 2020年第2期11卷 577-586页

作者： Bruno G.N.Andrade Flavia A.Bressani Rafael R.C.Cuadrat Polyana C.Tizioto Priscila S.N.de Oliveira Gerson B.Mourão Luiz L.Coutinho James M.Reecy James E.Koltes Paul Walsh Alexandre Berndt Julio C.P.Palhares Luciana C.A.Regitano Embrapa Southeast Livestock São CarlosBrazil Department of Molecular Epidemiology German Institute of Human Nutrition Potsdam-Rehbrücke(DIfE)NuthetalGermany NGS Genomic Solutions PiracicabaBrazil Department of Animal Science University of São Paulo/ESALQPiracicabaBrazil Department of Animal Science Iowa State UniversityAmesIAUSA NSilico Life Science DublinIreland

Background:The success of different species of ruminants in the colonization of a diverse range of environments is due to their ability to digest and absorb nutrients from cellulose,a complex polysaccharide found in leaves and grass.Ruminants rely on a complex and diverse microbial community,or microbiota,in a unique compartment known as the rumen to break down this polysaccharide.Changes in microbial populations of the rumen can affect the host’s development,health,and productivity.However,accessing the rumen is stressful for the animal.Therefore,the development and use of alternative sampling methods are needed if this technique is to be routinely used in cattle breeding.To this end,we tested if the fecal microbiome could be used as a proxy for the rumen microbiome due to its accessibility.We investigated the taxonomic composition,diversity and inter-relations of two different GIT compartments,rumen and feces,of 26 Nelore(Bos indicus)bulls,using Next Generation Sequencing(NGS)metabarcoding of bacteria,archaea and ciliate protozoa.Results:We identified 4265 Amplicon Sequence Variants(ASVs)from bacteria,571 from archaea,and 107 from protozoa,of which 143(96 bacteria and 47 archaea)were found common between both microbiomes.The most prominent bacterial phyla identified were Bacteroidetes(41.48%)and Firmicutes(56.86%)in the ruminal and fecal microbiomes,respectively,with Prevotella and Ruminococcaceae UCG-005 the most relatively abundant genera identified in each microbiome.The most abundant archaeal phylum identified was Euryarchaeota,of which Methanobrevibacter gottschalkii,a methanogen,was the prevalent archaeal species identified in both microbiomes.Protozoa were found exclusively identified in the rumen with Bozasella/Triplumaria being the most frequent genus identified.Co-occurrence among ruminal and fecal ASVs reinforces the relationship of microorganisms within a biological niche.Furthermore,the co-occurrence of shared archaeal ASVs between microbiomes indicates a dependency of the predominant fecal methano

关键词： archaea Bacteria Bos indicus Metabarcoding Methanobrevibacter Microbiome Microbiota

Dietary supplementation of Rosmarinus officinalis L.leaves in sheep affects the abundance of rumen methanogens and other microbial populations

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Journal of Animal Science and Biotechnology 2016年第4期7卷 514-521页

作者： Gabriella Cobellis Zhongtang Yu Claudio Forte Gabriele Acuti Massimo Trabalza-Marinucci Department of Veterinary Medicine University of Perugia Department of Animal Sciences The Ohio State University

Background： Rumen microbiome has a great influence on ruminant health and productivity. Different plant extracts have been tested for their ability to modulate the rumen microbiome to improve feed digestion and fermentation. Among the evaluated plant extracts, essential oils, tannins, and saponins appeared to have positive effects on rumen protein metabolism, volatile fatty acids production, and methane and ammonia production. Methods： The objective of this study was to evaluate the effect of rosemary （Rosmarinus officinalis L.） leaves and essential oils on rumen microbial populations. Four ruminally cannulated sheep were used in a 4x4 Latin square design fed （21 d/period）： 1） a control diet composed of alfalfa hay and concentrate pellet （CTR）, 2） CTR supplemented with 7 g/d/sheep of rosemary essential oil adsorbed on an inert support （EO）, 3） CTR with 10 g/d/sheep of dried and ground rosemary leaves （RL）, and 4） CTR with 10 g/d of dried and ground rosemary leaves pelleted into concentrate （RL pellet）. Abundance of total bacteria, archaea, protozoa, and some select bacterial species or groups was quantified using qPCR, while the community of bacteria and archaea was profiled using denaturing gradient gel electrophoresis. Results： No difference in abundance was noted for total bacteria, protozoa, or Rurninococcus flavefaciens between the control and the treatments, but the rosemary leaves, either in loose form or in pellet, decreased the abundance of archaea and the genus Prevotello （P 〈 0.001）. The rosemary leaves in loose form also decreased （P 〈 0.001） the abundance of Ruminococcus albus and Clostridium aminophilum, while the EO increased （P 〈 0.001） the abundance of Fibrobocter sucdnogenes. The community of bacteria and archaea was not affected by any of the supplements. Conclusions： Being able to affect the abundance of several groups of rumen microbes that are known to be involved in degradation of protein and fiber and production of methane and ammonia, rosemary leaves may be used to modulate rumen microbio

关键词： archaea Essential oil Plant extracts Rosemary Rumen microbiome

Metal-dependent anaerobic methane oxidation in marine sediment:insights from marine settings and other systems

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Science China(Life Sciences) 2019年第10期62卷 1287-1295页

作者： Lewen Liang Yinzhao Wang Orit Sivan Fengping Wang State Key Laboratory of Microbial Metabolism School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240 China Joint International Research Laboratory of Metabolic & Developmental Sciences Shanghai Jiao Tong UniversityShanghai 200240China Department of Geological and Environmental Sciences Ben-Gurion University of the NegevBeer-Sheva 84105Israel

Anaerobic oxidation of methane(AOM) plays a crucial role in controlling global methane emission. This is a microbial process that relies on the reduction of external electron acceptors such as sulfate, nitrate/nitrite, and transient metal ions. In marine settings, the dominant electron acceptor for AOM is sulfate, while other known electron acceptors are transient metal ions such as iron and manganese oxides. Despite the AOM process coupled with sulfate reduction being relatively well characterized,researches on metal-dependent AOM process are few, and no microorganism has to date been identified as being responsible for this reaction in natural marine environments. In this review, geochemical evidences of metal-dependent AOM from sediment cores in various marine environments are summarized. Studies have showed that iron and manganese are reduced in accordance with methane oxidation in seeps or diffusive profiles below the methanogenesis zone. The potential biochemical basis and mechanisms for metal-dependent AOM processes are here presented and discussed. Future research will shed light on the microbes involved in this process and also on the molecular basis of the electron transfer between these microbes and metals in natural marine environments.

关键词： anaerobic methane oxidation metal-AOM marine sediment archaea electron transfer

Editorial: Effects of metal contamination on ammonia-oxidizing microorganisms in a freshwater reservoir

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Journal of Environmental Sciences 2019年第5期31卷 364-366页

作者： Wei Feng Xiaowen Yan Chris Le Division of Analytical and Environmental Toxicology Department of Laboratory Medicine and Pathology Faculty of Medicine & Dentistry University of Alberta

Ammonia-oxidizing microorganisms,including ammoniaoxidizing bacteria(AOB)and archaea(AOA),are important to the global nitrogen cycle.These microbes catalyze the oxidization of ammonia(NH3)to nitrite(NO2-),the ratelimi... 详细信息

关键词： Accidental metal spill Ammonia-oxidizing archaea Ammonia-oxidizing bacteria amoA gene Arsenic,cadmium,copper,lead,zinc Lake sediment Nitrogen cycling

New approaches for archaeal genome-guided cultivation

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Science China Earth Sciences 2021年第10期64卷 1658-1673页

作者： Yinzhao WANG Yoichi KAMAGATA Meng LI Feifei HAN Fengping WANG Xiang XIAO State Key Laboratory of Microbial Metabolism School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China Bioproduction Research Institute National Institute of Advanced Industrial Science and Technology(AIST)Tsukuba 310-8555Japan Shenzhen Key Laboratory of Marine Microbiome Engineering Institute for Advanced StudyShenzhen 518052China Department of Surgery Massachusetts General Hospital and Harvard Medical SchoolBoston MA 02114USA School of Oceanography Shanghai Jiao Tong UniversityShanghai 200240China State Key Laboratory of Ocean Engineering Ocean and Civil EngineeringShanghai Jiao Tong UniversityShanghai 200240China

archaea,one of the three domains of life along with Bacteria and Eukarya,contains ancient life forms such as methanogen that are observed today on Earth,and one lineage Asgard archaea is also considered the closest ancestor of Eukarya.Recently,with the development of interdisciplinary studies from Earth and Life sciences,archaeal organisms are considered to play pivotal roles in geochemical cycling in nature.However,our understanding of the attributes,origin and evolution,geochemical and ecological functions of archaea is hampered by the scarcity of archaeal isolates,which has represented a challenge to researchers for the last 40 years.Cultivation-independent sequencing and phylogenomic analyses have demonstrated a considerable diversity of archaea with more than 20 novel phyla.However,only four archaeal phyla have cultured representatives,leaving large gaps in our knowledge of the metabolic capabilities and ecological functions of the majority of archaeal strains identified exclusively by DNA sequencing.In this review,we summarize the discovery and development of archaeal research,highlight the knowledge gap between uncultured and cultured archaeal microbes,and call on the importance of devoting greater research efforts to archaeal cultivation.Finally,we outlined new ideas and strategic approaches,namely,(1)genome-based methods,(2)microbial network information-based methods,(3)genome-scale model-guided methods,and(4)machine learning methods,to enable the cultivation of uncultivated archaeal microbes using accumulated high-throughput sequencing data.

关键词： archaea Cultivation Next-generation sequencing Uncultured archaea Genome Metabolic network

Lipidomics in archaeal membrane adaptation to environmental stresses and growth conditions:A review of culture-based physiological studies

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Science China Earth Sciences 2020年第6期63卷 790-807页

作者： Kai PLAW Xinxin LI Chuanlun ZHANG Shenzhen Key Laboratory of Marine archaea Geo-Omics Department of Ocean Science&EngineeringSouthern University of Science and TechnologyShenzhen 518055China SUSTech Academy for Advanced Interdisciplinary Studies Southern University of Science and TechnologyShenzhen 518055China Shanghai Sheshan National Geophysical Observatory and Research Station Shanghai 201600China

Membrane lipids are thought to be a crucial part of the homeoviscous adaptation of archaea to extreme conditions.This article reviews the recent lipidomic studies of physiological membrane adaptations of archaea,assesses the biomolecular basis of an organic paleothermometer,TEX86,and contemplates the future directions of archaeal lipidomics.The studies of extremophilic archaea have revealed that at least three different molecular mechanisms are involved in membrane adaptation of archaea:(1)regulation of the number of cyclopentane rings of caldarchaeol,(2)alteration of the diether-to-tetraether lipid ratio,and(3)variation of the proportion of saturated and unsaturated lipids.However,most of the studies have focused on a limited number of archaeal ether-linked lipids,such as glycerol dialkyl glycerol tetraethers(GDGTs),which only represent a fraction of the entire lipidome.Environmental factors such as growth temperature and pH have been most frequently reported,but biotic factors,including growth phases,nutrition,and enzymatic activities affecting the membrane lipid composition are often overlooked.Membrane lipids of mesophilic ammonia-oxidizing marine Thaumarchaeota have been applied in the reconstruction of past sea surface temperatures.However,recent culture-based physiological studies have demonstrated that non-thermal biotic factors,including dissolved oxygen,ammonia oxidation rate and the growth rate,are the main drivers of GDGT cyclization in Nitrosopumilus maritimus.Moreover,other related strains or ecotypes exhibit a markedly different set of stress adaptations.A trend is now developing to examine the whole lipid profile(lipidome)for studies of archaeal physiology and biochemistry related to lipid biosynthesis(lipidomics)to gain a better understanding of the biological mechanisms underpinning the applications of membrane lipid-based proxies in biogeochemical or ecological research.

关键词： archaea Lipidomics Environmental stress Mass spectrometry Organic paleothermometry Membrane bioenergetics

Long-term submergence of non-methanogenic oxic upland field soils helps to develop the methanogenic archaeal community as revealed by pot and field experiments

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Pedosphere 2020年第1期30卷 62-72页

作者： Takeshi WATANABE Susumu ASAKAWA Koichi HAYANO Graduate School of Bioagricultural Sciences Nagoya UniversityNagoya 464-8601(Japan) Kyushu National Agricultural Experiment Station NishigoshiKumamoto 861-1192(Japan)

The community structure of methanogenic archaea is relatively stable,i.e.,it is sustained at a high abundance with minimal changes in composition,in paddy field soils irrespective of submergence and drainage.In contrast,the abundance in non-methanogenic oxic soils is much lower than that in paddy field soils.This study aimed to describe methanogenic archaeal community development following the long-term submergence of non-methanogenic oxic upland field soils in pot and field experiments.In the pot experiment,a soil sample obtained from an upland field was incubated under submerged conditions for 275 d.Soil samples periodically collected were subjected to culture-dependent most probable number(MPN)enumeration,polymerase chain reaction-denaturing gradient gel electrophoresis(PCR-DGGE)analysis of archaeal 16 S r RNA gene,and quantitative PCR analysis of the methyl-coenzyme M reductase alpha subunit gene(mcr A)of methanogenic archaea.The abundance of methanogenic archaea increased from 102 to 103 cells g-1 dry soil and 104 to 107 copies of mcr A gene g-1 dry soil after submergence.Although no methanogenic archaeon was detected prior to incubation by the DGGE analysis,members from Methanocellales,Methanosarcinaceae,and Methanosaetaceae proliferated in the soils,and the community structure was relatively stable once established.In the field experiment,the number of viable methanogenic archaea in a rice paddy field converted from meadow(reclaimed paddy field)was monitored by MPN enumeration over five annual cycles of field operations.Viability was also determined simultaneously in a paddy field where the plow layer soil from a farmer’s paddy field was dressed onto the meadow(dressed paddy field)and an upland crop field converted from the meadow(reclaimed upland field).The number of viable methanogenic archaea in the reclaimed paddy field was below the detection limit before the first cultivation of rice and in the reclaimed upland field.Then,the number gradually increased over five years and finally reached 103–104 cell

关键词： denaturing gradient gel electrophoresis mcrA gene methanogenic archaea microbial community structure microbial habit most probable number method paddy field soil qPCR

Carbon Geochemistry of Gas Hydrate-associated Sediments in the Southwestern Taiwan Basin

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Acta Geologica Sinica(English Edition) 2018年第1期92卷 333-341页

作者： LEI Huaiyan YANG Yufeng Selvaraj KANDASAMY SHI Chunxiao State Key Laboratory of Marine Environmental Science Xiamen University Xiamen Fujian 361102 College of Ocean and Earth Sciences Xiamen University Xiamen Fujian 361102 Marine Technology Center of Huizhou Huizhou Guangdong 516008

Marine gas hydrates, one of the largest methane reservoirs on Earth, may greatly affect the deep sea sedimentary environment and biogeochemistry; however, the carbon geochemistry in gas hydrate-bearing sediments is poorly understood. In this study, we investigated the carbon variables in sediment core 973-3 from the southwestern Taiwan Basin in the South China Sea to understand the effect of environmental factors and archaeal communities on carbon geochemistry. The carbon profiles suggest the methanogenesis with the incerase of dissolved inorganic carbon （DIC） and high total organic carbon （TOC）（mean = 0.46%） originated from terrigenous organic matter （mean j13CToc value of -23.6%0） driven by the abundant methanogen ＇Methanosaeta and Methanomicrobiales＇. The active anaerobic oxidation of methane is characterized by the increase of DIC and inorganic carbon （IC）, and the depleted δ13CIC, coupled with the increase of TOC and the decrease of δ13Croc values owing to the methanotroph ＇Methanosarcinales/ANME＇ in 430-840 cm. Environmental factors and archaeal communities in core 973-3 are significantly correlated to carbon variables owing to methane production and oxidation. Our results indicate that the carbon geochemical characteristics are obviously responding to the formation and decomposition of gas hydrates. Furthermore, pH, Eh and grain size, and Methanosaeta greatly affect the carbon geochemistry in gas hydrate-associated sediments.

关键词： southwestern Taiwan Basin carbon geochemistry environmental conditions archaea gashydrate